At first, it seemed like federal prosecutors in southern Florida had their case against Dr. Ali Shaygan for illegally prescribing prescription painkiller in the bag. One of Shaygan's patients had died of an overdose, two undercover agents obtained numerous scripts from the doctor, and other patients were willing to testify.

Then the case began to unravel. The dead patient had a lot more coursing through his veins than just Shaygan's prescriptions. The more they investigated, the more it seemed like Shaygan's habits--things like meeting with patients at home or sometimes at coffee shops and squeezing patients into his schedule at the last minute--did not necessarily point to any wrongdoing. Shaygan's patients described him as attentive and detail-oriented--a high-quality doctor who cared about them and their health. And the defense was poking holes in the credibility of the lead DEA agent on the case.

Piling on 115 additional charges against Shaygan, which drew out the case and increased the complexity and expense of the defense;

Hiding important evidence from the defense;

Massaging witness statements to fit the prosecution's story;

Making up a story about witness tampering to launch an investigation into possible illegal behavior by the defense team that could have forced them to resign from the case;

Recruiting two witnesses as confidential informants for the prosecution and directing them to secretly record conversations with the defense team;

Hiding this secondary investigation, the recruitment of once-neutral witnesses into the government's camp, and the recordings from the defense and the court.

After less then 3 hours of deliberation by the jury, Shaygan was found not guilty on all 141 counts. And in his opinion yesterday, Judge Gold ordered the government to pay over half of Shaygan's defense fees. More importantly, he named and shamed the prosecutors and agents who violated the law and Department of Justice rules to win a conviction against Shaygan.

He may have been awarded over $600k by Judge Gold, but that's only a portion of the more than a million dollars the defense cost him and he hasn't received a dime of it yet and, should he get it at all, it will be a long time before he sees it. His life is likely in shambles, his name is ruined and his medical practice destroyed. And he was acquitted the first time around. This is the best it can get in our legal system.

The criminal law is a blunt tool, not a scalpel--something that legislators should keep in mind when they seek to apply it to all manner of conduct that is not traditionally criminal, like the practice of medicine. The result, inevitably, will be some degree of injustice, even when, as here, justice is ultimately served.

Update: Prof. Ellen Podgor asks of the DOJ's concession that it screwed up big-time, "But if this were a corporation that had committed misconduct, would these acknowledgments and payment be sufficient?"